The pandemic caused by SARS-CoV-2 led to a situation of home lockdown. Competitions, training, and sports activities were canceled for much of this period. This situation could have affected the physical and mental health and the mood states of young athletes. The aim of the study was to evaluate the variations in the mood states of young athletes of a highly competitive level during the different phases of lockdown in. The mood states of 45 Spanish youth athletes confined during the 10-week lockdown due to the COVID-19 pandemic -19 were assessed, using the Spanish-translated version of the POMS questionnaire, at the start of the home lockdown and at the start and at the end of the partial lockdown. The Total Mood Disturbance scores at week 10 were lower than those obtained in week 1 (pBonferroni = 0.031). The depression scores at week 6 (pBonferroni = 0.048) and at week 10 (pBonferroni < 0.001) were lower than those obtained in week 1. The confusion scores at week 10 were lower than those obtained in week 1 (pBonferroni = 0.002). These variations differed between team and individual sports. In conclusion, the lockdown produced changes in the young athletes’ mood states that should be considered when trying to optimize their physical and mental performance.